Skip to content

Batch Export

The Batch export plugin exports full FOV images, ROI crops, and single-cell crops to image files. It works in both standard and simple (images-only) viewer mode.

Export Modes

The plugin's Mode tabs select what you export:

Full FOV

Exports whole FOV renderings.

  • Export all FOVs (on by default) or pick specific FOVs from FOVs:.
  • Optional Figure width (px): / Figure height (px): overrides (0 = auto).

Single Cells

Exports cropped thumbnails centered on individual cells. Requires a cell table.

  • Filter (query): — a pandas-style query (e.g. marker > 0); click Apply.
  • Pick cells from Cells:, set Crop size (px): (default 128), and use Preview to check.

The Cells: list shows at most 500 cells

After Apply, only the first 500 matching rows are offered in the picker. The list gives no indication that it was truncated, so on a large table treat Filter (query): as the way to choose which cells you get — not as a pre-filter you then scroll through. Narrow the query until the population you want fits.

Simple viewer mode

Without a cell table, the Single Cells tab shows a notice and is unavailable. Full FOV and ROI export still work.

ROIs

Exports the crops for ROIs saved in the ROI manager.

  • Pick ROIs from ROIs:, optionally limited to the current FOV via Current FOV only.

Shared Options

These apply to whichever mode is active:

  • Marker set: — the channels/colors/contrast used for the render.
  • Output folder: (defaults to <base_folder>/exports) and Browse.
  • Format: — PNG, JPG, TIF, TIFF, or PDF.
  • Downsample: and DPI: (default 300).
  • Include scale bar and Scale bar % width: (1–10%, default 10).
  • Include annotations and Include masks (both on by default).
  • Mask outline px: — outline thickness.

Mask appearance

  • Masks only (black background) — render masks on black, without the channel image.
  • Mask layer:, Mask color:, and Mask opacity: (0–1) — set the color and opacity of a specific mask layer.
  • Override mask palette + Palette: — apply a saved palette instead of the current settings.

Exporting channels separately

  • Export channels separately — write one file per channel instead of a single composite.
  • Merge same color (enabled only when the above is on) — group channels that share a color into a single merged file.

Export Config Templates

Save a full set of export options for reuse. In the Export config templates accordion: type a Name: and click Save config; reload later from the Saved: dropdown with Load config (or Delete). Templates are stored under <base_folder>/.UELer/export_configs/.

Running an Export

Click Start to begin (or Cancel to stop). A progress bar tracks the run, and an Open output folder link appears when it finishes.

Output Filenames

Export Filename pattern
Full FOV <fov>.<format>
Single cell <fov>_cell_<label>.<format>
ROI (single FOV) <fov>_roi_<name-or-id>.<format>
ROI (map mode) map_<map_id>_roi_<name-or-id>.<format>
Separate channels <stem>_<channel>.<format>

Map-mode ROIs are rendered from the stitched map layer — see Map Mode.